changeset 10:b68fd88c0083 draft

Deleted selected files

--- a/data_manager_fastani.py	Sun May 29 20:33:37 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,102 +0,0 @@
-#!/usr/bin/env python
-# Errol Strain, [e-mail]
-# Database downloads for FastANI 
-
-import sys
-import os
-import tempfile
-import json
-import re
-import argparse
-import requests
-
-
-def download_D1(output_directory):
-
-    #FastANI databases from Kostas Lab 
-    url="http://enve-omics.ce.gatech.edu/data/public_fastani/D1.tar.gz"
-
-    cwd = os.getcwd() 
-    os.chdir(output_directory)
-
-    filename = url.split("/")[-1]
-    with open(filename, "wb") as f:
-      r = requests.get(url)
-      f.write(r.content)
- 
-    tarcmd="tar xvzf D1.tar.gz; rm -Rf D1.tar.gz"
-    os.system(tarcmd)
-
-    os.chdir(cwd)    
-   
-    return output_directory + "/D1"
-
-def download_VL(output_directory):
-
-    cwd = os.getcwd() 
-    os.chdir(output_directory)
-   
-    #FastANI uses filenames in output. Creating user friendly names
-    #for fish pathogens 
-    accdict={'NZ_CP018680':'Vibrio_harveyi_strain_QT520',
-      'SBIG01000001':'Vibrio_alginolyticus_strain_LF_TCBS_15',
-      'NZ_CP018311':'Vibrio_rotiferianus_strain_B64D1',
-      'NZ_CP032159':'Staphylococcus_warneri_strain_22_1',
-      'NZ_CP090968':'Edwardsiella_piscicida_strain_18EpOKYJ',
-      'NZ_CP044060':'Aeromonas_veronii_strain_FDAARGOS_632',
-      'NZ_AP022254':'Aeromonas_caviae_strain_WP8_S18_ESBL_04',
-      'NZ_CDBW01000001':'Aeromonas_sobria_strain_CECT_4245',
-      'NZ_CP018311':'Vibrio_rotiferianus_strain_B64D1'}
-
-    for acc in accdict: 
-      ecmd = "efetch -db nuccore -id " + acc + " -format fasta > " + accdict[acc] + ".fna"
-
-    os.chdir(cwd)    
-    return output_directory 
-
-
-def print_json (version,argspath,argsname,argsout):
-
-    data_table_entry = {
-      'data_tables' : {
-        'fastani': [
-          {
-            "value":version,
-            "name":argsname,
-            "path":argspath,
-          }
-        ]
-      }
-    }
-
-    with open(argsout, 'w') as fh:
-      json.dump(data_table_entry, fh, indent=2, sort_keys=True)
-        
-def main():
-   
-    parser = argparse.ArgumentParser(description='Download FastANI Databases')
-    parser.add_argument('--type', type=str, required=True, nargs=1, help='Database Type')
-    parser.add_argument('--desc', type=str, required=True, nargs=1, help='Database Description')
-    parser.add_argument('--out', type=str, required=True, nargs=1, help='output file')
-
-    args = parser.parse_args()
-
-    with open(args.out[0]) as fh:
-        params = json.load(fh)
-
-    output_directory = params['output_data'][0]['extra_files_path']
-    os.mkdir(output_directory)
-    data_manager_dict = {}
-
-    #Fetch the files and build blast databases
-    if(args.type[0]=="D1"):
-      output_directory=download_D1(output_directory)    
-      version="FastANI D1"
-    elif(args.type[0]=="VL"): 
-      output_directory=download_D1(output_directory)    
-      output_directory=download_VL(output_directory)    
-      version="FastANI D1 + VetLIRN"
-      
-    print_json(version,output_directory,args.desc[0],args.out[0])
-
-if __name__ == "__main__": main()